A soluble class I molecule analogous to mouse Q10 in the horse and related species

Horse serum is shown to contain a soluble class I molecule analogous to the secreted Q10 molecule in the mouse. This molecule has several similarities to the recently described mouse Q10 molecule: (1) it is smaller than membrane-bound equine class I molecules; (2) it occurs in a high molecular mass complex of 200–300 kd in serum; and (3) the serum levels of the equine molecule are similar to that of the Q 10 molecule (about 30 g/ml). A soluble molecule is also detected in the sera of species related to the horse; it has in fact been found in all the wild members of the order Perissodactyla so far tested. However, it was not detected in the serum of members of the orders Carnivora, Sirenia, Proboscidea, Artiodactyla, and Primates that were tested, nor in the serum of members of the order Rodentia other than in that of the genus Mus. Abbreviations used in this paper ₂m beta-2 microglobulin - PBS phosphate-buffered saline - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis     

Glutathione in plants: biosynthesis and physiological role in environmental stress tolerance

Glutathione (GSH; γ-glutamyl-cysteinyl-glycine) is a small intracellular thiol molecule which is considered as a strong non-enzymatic antioxidant. Glutathione regulates multiple metabolic functions; for example, it protects membranes by maintaining the reduced state of both α-tocopherol and zeaxanthin, it prevents the oxidative denaturation of proteins under stress conditions by protecting their thiol groups, and it serves as a substrate for both glutathione peroxidase and glutathione S-transferase. By acting as a precursor of phytochelatins, GSH helps in the chelating of toxic metals/metalloids which are then transported and sequestered in the vacuole. The glyoxalase pathway (consisting of glyoxalase I and glyoxalase II enzymes) for detoxification of methylglyoxal, a cytotoxic molecule, also requires GSH in the first reaction step. For these reasons, much attention has recently been directed to elucidation of the role of this molecule in conferring tolerance to abiotic stress. Recently, this molecule has drawn much attention because of its interaction with other signaling molecules and phytohormones. In this review, we have discussed the recent progress in GSH biosynthesis, metabolism and its role in abiotic stress tolerance.     

A CD44-like endothelial cell transmembrane glycoprotein (GP116) interacts with extracellular matrix and ankyrin.

We used complementary biochemical and immunological techniques to establish that an endothelial cell transmembrane glycoprotein, GP116, is a CD44-like molecule and binds directly both to extracellular matrix components (e.g., hyaluronic acid) and to ankyrin. The specific characteristics of GP116 are as follows: (i) GP116 can be surface labeled with Na 125I and contains a wheat germ agglutinin-binding site(s), indicating that it has an extracellular domain; (ii) GP116 displays immunological cross-reactivity with a panel of CD44 antibodies, shares some peptide similarity with CD44, and has a similar 52-kDa precursor molecule, indicating that it is a CD44-like molecule; (iii) GP116 displays specific hyaluronic acid-binding properties, indicating that it is a hyaluronic acid receptor; (iv) GP116 can be phosphorylated by endogenous protein kinase C activated by 12-O-tetradecanoylphorbol-13-acetate and by exogenously added protein kinase C; and (v) GP116 and a 20-kDa tryptic polypeptide fragment of GP116 from the intracellular domain are capable of binding the membrane-cytoskeleton linker molecule, ankyrin. Furthermore, phosphorylation of GP116 by protein kinase C significantly enhances GP116 binding to ankyrin. Together, these findings strongly suggest that phosphorylation of the transmembrane glycoprotein GP116 (a CD44-like molecule) by protein kinase C is required for effective GP116-ankyrin interaction during endothelial cell adhesion events.     

Different facets of a computational equivalent of genetic addition

This study deals with a biologically inspired system called DNA Addition System (DAS). The system consists of four elements: a chain molecule; a set of free (elemental) molecules, all of which refer to the elements of DNA; a quasi-free molecule, which is the last elemental molecule of the chain molecule; and a molecular machine. When the system works, a definite reconfiguration, referred to as addition, takes place. Addition actually adds a free molecule to the chain molecule to make it grow longer. The molecular machine decides which type of free molecule should be added taking into account the informational state of the system. A simulation model is also developed based on DAS to help generate chain molecule applying successive additions. This model can be used to simulate chain molecules that exhibit the characteristics of genetic molecules (i.e. molecules with identifiable segments) and behaviors of dynamical systems. How to correlate the characteristics of a dynamical system with the characteristics of DAS is also pointed out. Further study should be carried out to enhance the knowledge of DAS from both theory and application points of view.     

A new recombinant procoagulant protein derived from the cDNA encoding human factor VIII

We have constructed new B domain deletion derivatives of human factor VIII (FVIII) by manipulating the cDNA using recombinant DNA techniques. One of these new derivatives, FVIII delta II, in which amino acids 771(pro)-1666(asp) have been deleted, no longer contains the protease cleavage site at amino acid position 1648(arg)-1649(glu) known to be involved in the initial step of FVIII processing. We have expressed this molecule in both baby hamster kidney (BHK) 21 cells using the vaccinia virus (VV) expression system and have established Chinese hamster ovary (CHO) derived permanent cell lines expressing either recombinant (r)FVIII or FVIII delta II. The characteristics of FVIII delta II have been compared to those of rFVIII and/or plasma derived (pd) FVIII. FVIII delta II has the following properties: (i) it exhibits FVIII procoagulant activity; (ii) it is expressed at 5-fold higher levels than is the complete molecule in comparable systems; (iii) it migrates for the most part as a single major band on SDS-PAGE, in contrast to the complete molecule; (iv) it is activated to a greater extent by thrombin than is either rFVIII or pdFVIII; and (v) it retains the ability to bind von Willebrand factor (vWf).     

Amyloid precursor-like protein 2 association with HLA class I molecules

Amyloid precursor-like protein 2 (APLP2) is a ubiquitously expressed protein. The previously demonstrated functions for APLP2 include binding to the mouse major histocompatibility complex (MHC) class I molecule H-2K^d and down regulating its cell surface expression. In this study, we have investigated the interaction of APLP2 with the human leukocyte antigen (HLA) class I molecule in human tumor cell lines. APLP2 was readily detected in pancreatic, breast, and prostate tumor lines, although it was found only in very low amounts in lymphoma cell lines. In a pancreatic tumor cell line, HLA class I was extensively co-localized with APLP2 in vesicular compartments following endocytosis of HLA class I molecules. In pancreatic, breast, and prostate tumor lines, APLP2 was bound to the HLA class I molecule. APLP2 was found to bind to HLA-A24, and more strongly to HLA-A2. Increased expression of APLP2 resulted in reduced surface expression of HLA-A2 and HLA-A24. Overall, these studies demonstrate that APLP2 binds to the HLA class I molecule, co-localizes with it in intracellular vesicles, and reduces the level of HLA class I molecule cell surface expression.     

Identification and Molecular Characterization of a New Geminivirus Betasatellite Infecting Malvastrum coromandelianum in China

The complete nucleotide sequence of a satellite molecule associated with Malvastrum leaf curl Guangdong virus (MLCuGdV) infecting M. coromandelianum plants exhibiting leaf curl symptoms in a suburb of Guangzhou, Guangdong Province of China, is described and analysed. The molecule has typical features of betasatellites, containing a single ORF in the complementary‐sense strand, an A‐rich region, the satellite‐conserved region and a stem–loop structure. Compared with the geminivirus betasatellites in GenBank database, this molecule shows the highest nucleotide sequence identity of 71.9% with Tomato leaf curl Philippine betasatellite isolate Laguna1 (ToLCPB, AB307732). Phylogenetic analysis indicates that it is more related to isolate Laguna 1 and Laguna 2 of ToLCPB. According to the proposed species demarcation threshold of betasatellites (78% nucleotide identity), it is a novel betasatellite species, for which we propose the name Malvastrum leaf curl Guangdong betasatellite (MLCuGdB).     

Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (t_Thresh and d_Thresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems.     

Interaction of isopropylthioxanthone with phospholipid liposomes

Isopropylthioxanthone (ITX) is a highly lipophilic molecule which can be released in foods and beverages from the packages, where it is present as photoinitiator of inks in printing processes. Recently it was found in babies milk, and its toxicity cannot be excluded. The structure of the molecule suggests a possible strong interaction with the lipid moiety of biological membranes, and this is the first study of its effects on phospholipid organization, using differential scanning calorimetry (DSC) and spin labelling techniques. The data obtained with multilamellar liposomes of saturated phospholipids of different length, with and without cholesterol, point out that the molecule changes the lipid structure; in particular, in the gel state, behaving like a disordering agent it increases the mobility of the bilayer, while, in the fluid state, tends to rigidify the membrane, in a cholesterol like way. This behavior supports the hypothesis that ITX experiences a relocation process when the lipid matrix passes from the gel to the fluid state.     

Mn(II) binding sites of calf liver arginase

Commercial calf liver arginase was further purified through gel filtration column chromatography. The enzyme is nearly homogeneous in SDS-PAGE; it contains 4 manganese atoms per molecule of enzyme. By dialysis against 1,10-o-phenanthroline at 4°C it is possible to obtain an arginase apo-form containing 2 manganese atoms per molecule of enzyme (apo-2 form) while a treatment of the pur enzyme with o-phenanthroline at 37°C followed by dialysis against 0.1 M NaCl is capable of producing an apoenzyme with only 1 manganese atom per molecule (apo-1 form). The apo-2 and apo-1 arginases retain respectively about 50% and 25% of the full enzymatic activity. NMR titrations of both apo-arginases with increasing concentrations of manganese allowed us to determine the affinity constants for the binding of Mn²⁺ to the protein. It was shown that in this enzyme two manganese atoms are weakly bound, one is more strongly bound and the fourth one is bound so tightly that it is not removed under the experimental conditions used.     

Sequence and conformation of 5 S RNA from Chlorella cytoplasmic ribosomes: comparison with other 5 S RNA molecules

The sequence of Chlorella cytoplasmic 5 S RNA has been determined by fingerprinting techniques. Partial digests were fractionated by a two-dimensional acrylamide gel electrophoretic technique, which indicates whether specific fragments are paired in the molecule. In this way, the four main base-paired regions of the molecule were located. The sequence of Chlorella cytoplasmic 5 S RNA is related to, but different from, that of other eukaryotic 5 S RNAs: it shows approximately 60% homology with vertebrate 5 S RNA and 40% homology with yeast 5 S RNA. In some respects the conformation of the molecule in solution is quite different from that of other sequenced 5 S RNAs: in particular, the highly accessible region found around position 40 in all other 5 S RNAs (prokaryotic and eukaryotic) does not exist in this molecule.     

A spectrophotometric study of Penicillium brevicompactum RNAase complex formation with adenine nucleotides]

Spectrophotometric study of extracellular Pen. brevicompactum RNAse interaction with adenyl nucleotides and constituents have been carried out. It is states that: 1) complex RNAse--nucleotide is formed by association of one enzyme molecule with one nucleotide molecule; 2) all the nucleotide components base sugar and phosphate, take part in the formation of this complex; 3) for the effective association of this complex it is necessary to have a high correspondence (complementaryty) of nucleotide geometric configuration to the space composition of the active site of RNAse.     

Water-soluble form of RT1.A class I MHC molecules in the kidney and liver of the rat

The RT1.A (H-2K,D type) class I major histocompatibility complex (MHC) antigens of the rat are well recognized as membrane-bound glycoproteins. In this report, we demonstrate that liver and kidney in the DA rat strain contain large amounts of a water-soluble RTl. A class I molecule with a discrete heavy chain approximately 5 kd smaller than the membrane-bound form. An identical molecule could be identified in DA rat serum. This small class I molecule carries all of the polymorphic antigenic determinants of the RT1.A^av1 class I molecule. The water-soluble molecule is readily denatured in its pure form when frozen and thawed, but this does not occur when it is mixed with serum, presumably because of a stabilizing interaction with one or more carrier proteins. The half-life of the class I molecule in serum was measured to be approximately 1.5 h. The LEW rat strain produced detectable but substantially smaller amounts of water-soluble RT1.A molecules. Our studies indicate that RT1.A^av1 class I MHC antigens are synthesized and presumably secreted in a smaller water-soluble form by liver, kidney, and possibly other tissues under physiological conditions, a point of con-siderable interest in view of the immunoregulatory functions of the membrane-bound forms of these molecules.     

Shedding light on the EpCAM: An overview

The epithelial cell adhesion molecule (EpCAM) is a Type I transmembrane superficial glycoprotein antigen that is expressed on the surface of basolateral membrane of multiple epithelial cells with some exceptions such as epidermal keratinocytes, hepatocytes, thymic cortical epithelial cells, squamous stratified epithelial cells, and myoepithelial cells that do not express the molecule. The molecule plays a pivotal role in the structural integrity, adhesion of the epithelial tissues and their interaction with the underlying layers. EpCAM prevents claudin-7 and claudin-1 molecules from degradation, thereby, decreasing the number of tight junctions and cellular interconnections, and promoting the cells toward carcinogenic transformation. Moreover, the mutations in the EpCAM gene lead to congenital tufting enteropathy, severe intestinal epithelium homeostasis disorders, and Lynch and Lynch syndrome. Overexpression of EpCAM on stem cells of some cancers and the presence of this molecule on circulating tumor cells (CTCs) makes it a promising candidate for cancer diagnosis as well as tracing and isolation of CTCs.     

Probing the effect of electric field in 9,10-dimethoxy-2,6-bis(2-p-tolylethynyl)anthracene molecular nanowire using quantum chemical and charge density analysis

The effect of electric field (EF) in a newly designed molecular nanowire 9,10-dimethoxy-2,6-bis(2-p-tolylethynyl)anthracene has been analysed theoretically from the structural and electronic charge transport properties using quantum chemical and charge density calculations. The applied EF (0–0.36 VÅ^? 1) alters the molecular conformation, charge density distribution, electrostatic properties and the electronic energy levels of the molecule. Furthermore, the applied EF decreases the highest occupied molecular orbital–lowest unoccupied molecular orbital gap significantly from 1.775 to 0.258 eV and it also induces polarisation in the molecule, which leads to increase the dipole moment of the molecule. The electrostatic potential for various levels of applied EF reveals the charge-accumulated regions of the molecule. The I–V characteristics of the molecule have been studied against various applied fields using Landauer formalism.     

Nitric oxide as a key component in hormone-regulated processes

Nitric oxide (NO) is a small gaseous molecule, with a free radical nature that allows it to participate in a wide spectrum of biologically important reactions. NO is an endogenous product in plants, where different biosynthetic pathways have been proposed. First known in animals as a signaling molecule in cardiovascular and nervous systems, it has turned up to be an essential component for a wide variety of hormone-regulated processes in plants. Adaptation of plants to a changing environment involves a panoply of processes, which include the control of CO₂ fixation and water loss through stomatal closure, rearrangements of root architecture as well as growth restriction. The regulation of these processes requires the concerted action of several phytohormones, as well as the participation of the ubiquitous molecule NO. This review analyzes the role of NO in relation to the signaling pathways involved in stomatal movement, plant growth and senescence, in the frame of its interaction with abscisic acid, auxins, gibberellins, and ethylene.     

The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature

In general, it is not easy to specify a single sequence identity for each molecule name that appears in a pathway in the scientific literature. A molecule name may stand for concepts of various granularities, from concrete objects such as H-Ras and ERK1 to abstract concepts or categories such as Ras and MAPK. Typically, the relations among molecule names derive a hierarchical structure; without a proper way to handle this knowledge, it becomes ever more difficult to develop a reliable pathway database. This paper describes an ontology that is designed to annotate molecules in the scientific literature on signal transduction pathways.     

Double-sides sticking mechanism of vinblastine interacting with α,β-tubulin to get activity against cancer cells

Abstract

Vinblastine (VLB) and its derivatives have been used for clinical first-line drugs to treat various cancers. Due to the resistance and serious side effects from using VLB and its derivatives, there is a need to discover and develop novel VLB derivatives with high activity against cancer cells. In order to better discover and develop new VLB derivatives, we need to study the structural basis of VLB's anti-cancer cytotoxicity and the mechanism of its interaction with α,β-tubulins. Based on the crystal structure of α,β-microtubule complex protein, the molecular dynamics method including the sampling PMF method was used to study the variation of dissociation free energy (ΔG) of α,β-tubulins under different system conditions, and then from which to study the mechanism of the interaction between VLB and α,β-tubulins. The obtained results show that the dissociation of pure α,β-tubulins requires 197.8?kJ·mol^?1 for ΔG. When the VLB molecule exists between the interface of α,β-tubulins, the dissociation ΔG of α,β-tubulins reaches 220.5?kJ·mol^?1, which is greater than that of pure α,β-tubulin. The VLB molecule is formed by connecting a vindoline moiety (VM) molecule with a catharanthine moiety (CM) molecule through a carbon-carbon bond, which is a larger molecule. When the CM molecule exists in the middle of α,β-tubulin interface, the dissociation ΔG of α,β-tubulins is 46.2?kJ·mol^?1, during which the CM moves with β-tubulin. When the VM molecule exists between the middle of α,β-tubulin interface, the dissociation ΔG of α,β-tubulins is 86.7?kJ·mol^?1, during which it moves with α-tubulin. Therefore, the VLB molecule is like a double-sides tape to stick α-tubulin and β-tubulin together. The VLB molecule intervenes the dynamic equilibrium between dissociation and aggregation of α-tubulin and β-tubulin by a double-sides sticking mechanism to exert high activity with toxicity against cancer cell. Besides, our results demonstrate that VLB has its structural basis for anticancer cytotoxicity due to its two compositions composed of a CM molecule and a VM molecule although they have little toxicity against cancer cell alone.     

Some Thoughts about Bond Energies,Bond Lengths,and Force Constants

The bond energy (BE) of a polyatomic molecule cannot be measured and, therefore, determination of BEs can only be done within a model using a set of assumptions. The bond strength is reflected by the intrinsic BE (IBE), which is related to the intrinsic atomization energy (IAE) and which represents the energy of dissociation under the provision that the degree of hybridization is maintained for all atoms of the molecule. IBE and BE differ in the case of CC and CH bonds by the promotion, the hybridization, and the charge reorganization energy of carbon. Since the latter terms differ from molecule to molecule, IBE and BE are not necessarily parallel and the use of BEs from thermochemical models can be misleading. The stretching force constant is a dynamical quantity and, therefore, it is related to the bond dissociation energy (BDE). Calculation and interpretation of stretching force constants for local internal coordinate modes are discussed and it is demonstrated that the best relationship between BDEs and stretching force constants is obtained within the model of adiabatic internal modes. The valence stretching force constants are less suitable since they are related to an artificial bond dissociation process with geometrical relaxation effects suppressed, which leads to an intrinsic BDE (IBDE). In the case of AX_n molecules, symmetric coordinates can be used to get an appropriate stretching force constant that is related to the BE. However, in general stretching force constants determined for symmetry coordinates do not reflect the strength of a particular bond since the related dissociation processes are strongly influenced by the stability of the products formed.